Contacts of the helix formed by residues 266 - 279 (chain B) in PDB entry 4Z2C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B MET 3.8 9.9 + - - -
111B ASP* 3.3 12.3 + - - -
112B GLY* 3.2 30.7 - - - +
264B MET 4.3 0.6 + - - -
265B VAL* 1.3 76.8 - - - +
267B LYS* 1.3 61.4 + - - +
268B THR* 2.9 29.7 + - - -
269B LYS* 3.7 25.3 - - + +
270B VAL* 3.0 29.3 + - - +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B MET* 5.0 5.9 + - + +
111B ASP* 3.9 15.1 + - - +
261B PHE* 3.7 37.9 - - + -
265B VAL 3.7 4.4 + - - -
266B ASN* 1.3 73.7 + - - +
268B THR* 1.3 57.6 + - - +
270B VAL* 3.5 4.2 + - - +
271B HIS* 2.9 28.2 + - - +
291B ASP* 4.1 16.2 - - - +
293B SER* 5.9 2.5 - - - +
298B VAL* 6.1 0.7 - - + -
300B PHE* 4.0 6.2 - - + -
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 3.3 31.1 + - - +
266B ASN* 2.9 12.9 + - - -
267B LYS* 1.3 75.8 - - - +
269B LYS* 1.3 61.2 + - - +
271B HIS* 3.1 11.2 + - + +
272B GLU* 2.9 46.5 + - + +
291B ASP* 5.1 4.4 + - - -
447D ARG* 5.2 4.7 + - - -
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Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASN* 3.4 26.1 + - + +
268B THR* 1.3 78.8 - - - +
270B VAL* 1.3 57.5 + - - +
272B GLU* 3.3 14.8 + - - +
273B HIS* 2.9 30.4 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 4.3 18.2 - - + -
265B VAL* 5.1 4.7 - - + -
266B ASN 3.0 18.1 + - - +
267B LYS* 3.6 8.3 - - - +
269B LYS* 1.3 73.6 - - - +
271B HIS* 1.3 61.3 + - - +
273B HIS* 3.9 4.9 - - - +
274B ILE* 2.9 31.4 + - - +
300B PHE* 5.1 3.8 - - + -
321B THR* 5.4 11.6 - - + +
323B MET* 5.4 7.9 - - + +
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS 2.9 15.9 + - - +
268B THR* 3.2 13.7 - - + +
270B VAL* 1.3 75.8 - - - +
272B GLU* 1.3 58.7 + - + +
274B ILE* 3.2 4.7 + - - +
275B VAL* 2.9 46.1 + - + +
289B VAL* 3.3 34.8 + - + +
290B ARG* 5.0 0.4 - - - -
291B ASP* 4.4 16.5 + - + +
300B PHE* 4.0 24.1 - + + -
406D GLY* 5.4 7.7 - - - -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B THR* 2.9 35.3 + - + +
269B LYS* 3.6 13.0 - - - +
271B HIS* 1.3 77.7 - - + +
273B HIS* 1.3 57.1 + - - +
275B VAL* 3.3 7.5 + - - +
276B ARG* 2.9 29.0 + - - +
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LYS 2.9 18.1 + - - +
270B VAL* 4.0 5.6 - - - +
272B GLU* 1.3 76.1 - - - +
274B ILE* 1.3 59.1 + - - +
276B ARG* 3.4 20.5 + - + +
277B LEU* 2.9 35.0 + - + +
320B MET* 4.5 9.2 - - + -
321B THR* 4.4 32.5 - - + +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B VAL 2.9 20.3 + - - +
271B HIS* 3.5 7.9 - - - +
273B HIS* 1.3 76.1 - - - +
275B VAL* 1.3 60.9 + - + +
277B LEU* 3.4 6.4 + - - +
278B VAL* 2.9 27.4 + - - +
283B ILE* 5.8 1.6 - - - +
289B VAL* 6.1 4.9 - - + -
300B PHE* 5.9 3.6 - - + -
321B THR* 5.9 6.5 - - + +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B HIS* 2.9 43.2 + - + +
272B GLU* 3.7 7.0 - - - +
274B ILE* 1.3 74.0 - - + +
276B ARG* 1.3 63.3 + - - +
278B VAL* 2.8 22.8 + - + +
279B GLN* 2.9 15.8 + - + +
289B VAL* 5.5 4.0 - - + -
407D LEU* 3.6 44.0 - - + +
408D GLU 4.8 4.5 - - - +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLU 2.9 17.9 + - - +
273B HIS* 3.5 23.1 - - - +
275B VAL* 1.3 78.5 - - - +
277B LEU* 1.3 60.7 + - - +
278B VAL 3.6 0.2 + - - -
279B GLN* 3.8 10.5 + - - +
280B GLU* 3.8 11.8 - - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B HIS* 2.9 27.8 + - + +
274B ILE* 3.8 7.0 - - - +
276B ARG* 1.3 74.6 - - - +
278B VAL* 1.3 63.5 + - - +
280B GLU* 3.6 12.3 + - - +
282B ARG* 3.6 32.8 + - + +
283B ILE* 3.9 6.9 + - + -
320B MET* 5.8 7.6 - - + -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE 2.9 13.1 + - - +
275B VAL* 2.8 16.0 + - + +
277B LEU* 1.3 75.8 - - - +
279B GLN* 1.3 57.5 + - - +
280B GLU 3.0 10.0 + - - -
281B LYS* 3.6 10.2 + - - -
283B ILE* 4.6 20.8 - - + +
286B ILE* 6.3 2.5 - - + -
407D LEU* 5.6 7.9 - - + -
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B VAL* 2.9 14.7 + - + +
276B ARG* 3.8 6.2 + - - +
277B LEU 3.5 0.2 - - - -
278B VAL* 1.3 73.8 - - - +
280B GLU* 1.3 58.4 + - - +
281B LYS 3.8 0.4 - - - -
407D LEU* 5.2 10.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il